Showing : proteomics • reset
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123
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limma/voom for protein intensity data
limma proteomics voom
updated 8 days ago by ▴ 840 • written 8 days ago by ▴ 60
0
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1
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76
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 22 days ago by 43k • written 23 days ago by • 0
0
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5
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131
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 27 days ago by 43k • written 27 days ago by • 0
0
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0
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52
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How to handle the imputation and normalisation?
Proteomics DEP limma
5 weeks ago barrypraveen • 0
0
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1
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112
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How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 8 weeks ago by • 0 • written 9 weeks ago by • 0
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101
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what is the difference between iBAQ or LFQ?
Proteomics DEP limma
10 weeks ago • updated 9 weeks ago barrypraveen • 0
0
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4
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199
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How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
12 weeks ago barrypraveen • 0
4
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3
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413
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Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 6 months ago by 43k • written 6 months ago by ▴ 10
5
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6
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404
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 6 months ago by 43k • written 6 months ago by ▴ 10
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170
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Limma design multi-level experiment with 3 time points
R proteomics limma
6 months ago ellen2270 • 0
0
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4
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243
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
6 months ago rina ▴ 20
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203
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
7 months ago Robert Castelo ★ 2.7k
2
votes
1
reply
354
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 7 months ago by 58k • written 7 months ago by ★ 1.5k
0
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288
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Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
9 months ago Laura • 0
1
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2
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227
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calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
9 months ago Oliver • 0
0
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3
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235
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Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
9 months ago Gilad • 0
1
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2
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235
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error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 9 months ago by ▴ 40 • written 9 months ago by • 0
5
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6
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374
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possible package naming conflict
proteomics
9 months ago Tobias ▴ 30
1
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0
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197
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News: Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow proteomics Proteome
9 months ago info ▴ 10
0
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0
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138
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Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
9 months ago yueli7 ▴ 10
0
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1
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268
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R package to change protein *.msf file to any readable file
Proteome ProteomicsWorkflow proteomics
updated 10 months ago by ▴ 850 • written 10 months ago by ▴ 10
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0
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225
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Job: Data Scientist Proteomics (100%), Biozentrum, University of Basel, Switzerland
Switzerland JobPosting Basel Proteomics
10 months ago Robert Ivanek ▴ 700
0
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3
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354
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Find DEPs among TMT labeling proteom time course data by limma
limma proteomics TMTlabeling timecoursedata
updated 10 months ago by ▴ 270 • written 10 months ago by • 0
3
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0
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429
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
11 months ago Johannes Rainer ★ 1.9k
2
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0
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245
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Job: PostDoc position for the analysis of large scale metabolomics data
metabolomics proteomics Job
12 months ago Johannes Rainer ★ 1.9k
1
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6
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689
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DEP package: Problems installing on macOS
software error DEP proteomics
updated 14 months ago by 1.5k • written 14 months ago by • 0
0
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0
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499
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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
software engineer RNASeq proteomics Job visualisation
15 months ago Laurent Gatto 1.5k
0
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0
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138
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How to generate custom MS database using CustomProDB?
r proteomics
16 months ago nattzy94 • 0
2
votes
1
reply
246
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Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
18 months ago daniel.magnus.bader ▴ 40
2
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1
reply
204
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Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
18 months ago harelarik ▴ 50
1
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0
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220
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News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
19 months ago Laurent Gatto 1.5k
1
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2
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483
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Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
20 months ago Rob • 0
0
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0
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281
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
20 months ago lhuang7 ▴ 50
3
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0
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1.5k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
22 months ago • updated 21 months ago Gordon Smyth 43k
0
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0
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411
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News: May Institute Computation and statistics for mass spectrometry and proteomics
conference mass spectrometry proteomics News
21 months ago shepherl 2.8k
0
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0
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388
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News: course - Protemics with R and Bioconductor - 17-19 February 2020 in Berlin
Bioconductor R Proteomics News
22 months ago info ▴ 10
0
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0
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180
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proteoQC throwing error after running
ProteoQC Proteomics
22 months ago laural710 • 0
0
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2
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457
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Total Area Sum Intensity based Normalization for label-free quantitative proteomics
normalization proteomics label-free
22 months ago amolares • 0
0
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3
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438
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Writing a loop through multiple fasta files and named files (is it possible with MSGFplus?)
MSGF+ Proteomics r
updated 23 months ago by 25k • written 23 months ago by • 0
0
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0
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213
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DEP package - Understanding the results table
dep proteomics logFC
23 months ago rina ▴ 20
0
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0
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293
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DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
2.0 years ago • updated 23 months ago dparrine • 0
2
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0
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1.6k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
24 months ago Laurent Gatto 1.5k
0
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0
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245
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News: Protemics with R and Bioconductor course in Berlin
R Proteomics News
2.0 years ago info ▴ 10
0
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0
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286
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Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
2.1 years ago tatabox • 0
0
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8
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1.3k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 2.1 years ago by • 0 • written 3.7 years ago by ▴ 20
3
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3
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440
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Clarification of results tables in DEP
DEP proteomics
updated 2.1 years ago by ▴ 70 • written 2.2 years ago by ▴ 480
1
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3
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414
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Interpreting Fold Change Calculation in Limma to Non-Statisticians: Sanity Check
Limma proteomics limma
updated 2.3 years ago by • 0 • written 2.3 years ago by • 0
2
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2
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347
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Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
r proteomics RNA-Seq
updated 2.5 years ago by ▴ 180 • written 2.5 years ago by ▴ 10
0
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0
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296
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How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
2.5 years ago Wuschel ▴ 10
0
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2
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374
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Comparative proteome analysis of two different species
proteomics LC-MS/MS
updated 2.5 years ago by 1.5k • written 2.5 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Volcano plots of DEGs from Swish are weird by Qin ▴ 10
Thans for your reply. I'm sorry for reply so late, because I didn't getting any messages in my email. I will read details of the vignette.
Comment: At least one covariate is confounded with batch! Please remove confounded covari by NewBioInfo • 0
Thank you, James. I was indeed using the wrong matrix. The `nonExtimable` did give me the column name which was causing the issue but I do …
Comment: Returning to edgeR version 3.26.1? by Gordon Smyth 43k
I don't think that any changes to edgeR between 3.26.1 and 3.26.8 could have caused the changes that you show.
Comment: Returning to edgeR version 3.26.1? by mvanhorn • 0
Thank you very much for your reply! Our project is a reanalysis of large sets of RNA-seq data to identify circular RNAs using the CIRIquan…
Comment: "full model matrix is less than full rank" by ATpoint ▴ 840
My best guess is that young and old are not "young" or "old" but include some hidden whitespaces like " young" or "old ". That would then m…
Votes
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: Swish direction of comparison based on order of factors
Comment: Gradient dotplot
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Awards • All
Scholar to Gordon Smyth 43k
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Popular Question to Hervé Pagès 15k
Scholar to Jiang, Mike ★ 1.3k
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